rs900238

Variant names:

• chr8-48683498-C-T
• rs900238
• ENST00000522575.1:n.357-11926C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522575.1(ENSG00000253608):​n.357-11926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,056 control chromosomes in the GnomAD database, including 36,091 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (36091 hom., cov: 32)
• Consequence: ENSG00000253608 ENST00000522575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 3 publications found

Genes affected

ENSG00000253608 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522575.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929268	NR_105002.1		n.357-11926C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253608	ENST00000522575.1	TSL:2	n.357-11926C>T		intron	N/A
	ENSG00000253608	ENST00000654201.1		n.58-11253C>T		intron	N/A
	ENSG00000253608	ENST00000657307.2		n.173-11926C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98361 AN: 151938 Hom.: 36094 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.647 AC: 98382 AN: 152056 Hom.: 36091 Cov.: 32 AF XY: 0.651 AC XY: 48377 AN XY: 74338

African (AFR) AF: 0.278 AC: 11536 AN: 41462

American (AMR) AF: 0.657 AC: 10039 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2385 AN: 3472

East Asian (EAS) AF: 0.716 AC: 3692 AN: 5160

South Asian (SAS) AF: 0.637 AC: 3063 AN: 4812

European-Finnish (FIN) AF: 0.868 AC: 9182 AN: 10582

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56195 AN: 67980

Other (OTH) AF: 0.656 AC: 1381 AN: 2104

Alfa AF: 0.757 Hom.: 24407

Bravo AF: 0.617

Asia WGS AF: 0.637 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		-0.037

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs900238; hg19: chr8-49596058;